Wednesday, February 07, 2018

The Salzburg sixty discuss a new paradigm in genetic variation

Sixty evolutionary biologists are going to meet next July in Salzburg (Austria)to discuss "a new paradigmatic understanding of genetic novelty" [Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses]. You probably didn't know that a new paradigm is necessary. That's because you didn't know that the old paradigm of random mutations can't explain genetic diversity. (Not!) Here's how the symposium organizers explain it on their website ...

For more than half a century it has been accepted that new genetic information is mostly derived from random‚ error-based’ events. Now it is recognized that errors cannot explain genetic novelty and complexity.

The older concepts we have now for a half century cannot sufficiently explain the complex tendency of the genetic code. They can't explain the functions of mobile genetic elements and the endogenous retroviruses and non-coding RNAs. Also, the central dogma of molecular biology has been falsified -- that is, the way is always from DNA to RNA to proteins to anything else, or the other "dogmas," e.g., replication errors drive evolutionary genetic variation, that one gene codes for one protein and that non-coding DNA is junk. All these concepts that dominated science for half a century are falsified now. ...

Here's a summary of where my views differ ...

The fundamental concepts in evolution and molecular biology were worked out in the middle of the last century and thery have been steadily improved and modified since then. They are fully capable of explaining mobile genetic elements, endogenous retroviruses, and non-coding RNAs. Read any textbook.

The Central Dogma of Molecular Biology says that once information is transferred to protein it can't go back to nucleic acids [Central Dogma of Molecular Biology]. It's blatantly obvious that Günther Witzany doesn't understand the Central Dogma. It's obvious that he hasn't read Crick's papers.

The idea that replication errors create genetic variation has not been falsified. It is by far the most important source of mutation.

The idea that one gene codes for one protein is a false strawman version of our current understanding of a gene [What Is a Gene?]. No knowledgeable scientist ever thought that all genes produced proteins and no knowledgeable scientist since 1980 was unaware of genes encoding multiple proteins. Read a textbook.

No knowledgeable scientist ever said that all non-coding DNA is junk. They do, however, say that most of the DNA in the human genome is junk. That's a concept that was formed in the middle of the last century and has become more and more true as evidence accumulates in the 21st century. It has not been falsified as Günther Witzany claims. He has not been keeping up with the scientific literature.

Nobody is questioning the fact that transposons and viruses can cause mutations and genomic rearrangements. The only serious debate is over the frequency of such events. By looking at the amount of variation in individual humans, scientists have determined that 99.9% of all variation is in the form of single nucleotide changes (SNPs) or small (1-10 bp) insertions/deletions. Larger differences due to transposons and viral insertions/deletions account for only 0.1% of the total [Genetic variation in human populations]. All sorts of mutations will contribute to evolution in the long run but it's absurd to think there's any "paradigm shift" in the making. Instead, this is a classic example of a paradigm shaft (a term coined by Diogenes on an earlier Sandwalk post).

I can't see why variations caused by changes in regulatory networks, and changes due to viruses getting into the genome, cannot be due to these being random changes that are then selected for or against. Witzany's wording makes it sound as if he somehow knows that the changes are carefully planned by some grander regulatory mechanism. I do hope he will enlighten us as to how that works.

Of course, he will definitely call for the replacement of the current understanding of evolutionary mechanisms by a New Paradigm. After all, everybody does, and their new paradigms seem to rapidly replace one another.

Witzany is a big fan of Jim Shapiro, who is invited to the meeting. If you read Shapiro's writings you come away with the same problem you mention. It seems as though he's invoking some higher power that creates organisms designed to evolve by "natural genetic engineering."

This is why the IDiots are such big fans of Shapiro and The Third Way. The thirders had to put a disclaimer on their website distancing themselves from creationists but methinks they doth protest too much.

A capability for "natural genetic engineering", even if it existed, would rapidly be lost by mutation unless it created a great genetic advantage fairly often. If it was needed only once every 100,000 years it would be lost by mutation before next time.

They need to explain why, even if it existed, it stayed around. Of course, they have to find it first.

I think one should not expect the meeting to be a festival of Iconoclasts.

Skimming through the list of speakers I discovered many (as far as I can tell) respected scientists accompanied by, as I suspect, a few outliers (including the organizer and Sharpiro).

I for example very much doubt that Koonin agrees with most of Witzanys statements you cited. I never understood why he associates himself with this 'Third Way Club' In addition I would consider Eric Westhofs views (I worked in his department) very similar to the views of our host.Just to mention two....

I agree that prophesying paradigm changes before they have happened is very poor form in trying to suggest new ideas. I see it a lot actually.

YEt, i say yet, all this mutationism , random etc etc, as being the origin of new genetic information and so the origin for biological complexity and diversity.So much was never placed on so unlikely a mechanism.Yet its the finale gasp and grasp of evolutionism in its claims to legitimacy.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.